Commits for hiram

v425_preview2 to v425_base (2021-12-20 to 2022-01-10) v425

cf8389dd02c2c67d1424737f932db4c8b53efd12 Mon Dec 20 15:26:34 2021 -0800

• adding in a number of mammal assemblies from the Zoonomia project most already outdated by same assembly in mammals hub no redmind
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 53, context: html, text, full: html, text

2057fe2ab96405f0107a695de71fa9ea1427b0ec Mon Dec 20 18:34:55 2021 -0800

• recording the translation list no redmine
  • src/hg/makeDb/doc/zoonomiaAsmHub/zoo241.asmId.sciName.tsv - lines changed 241, context: html, text, full: html, text

d79d3e1568e732852f341062f1604b7484572d8f Mon Dec 20 21:27:53 2021 -0800

• now using fully qualified domain name to dynablat-01 refs #28654
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 10, context: html, text, full: html, text

5beab349a3b593b600526dd7445c63ebff31d13b Mon Dec 20 21:29:24 2021 -0800

• adding many new hubs for Zoonomia 241-way no redmine
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 167, context: html, text, full: html, text

571d56486794183897e7eb88719fe1025d1ea442 Mon Dec 20 21:32:19 2021 -0800

• up to date with zoonomia added no redmine
  • src/hg/makeDb/doc/asmHubs/hgdownload.index.html - lines changed 30, context: html, text, full: html, text

efcb7334402bd922fa514a2b967ffa3843dd02db Wed Dec 22 09:17:04 2021 -0800

• adding fungi and specifics for augustus species and rmskSpecies no redmine
  • src/hg/makeDb/doc/asmHubs/runBuild - lines changed 29, context: html, text, full: html, text

c2d8f10c6d0ce5ebb68e8a76c5d9a2e94ab3dcd8 Tue Dec 28 15:51:34 2021 -0800

• correct ncbiGene procedure and correctly run up unplaced contig assembly when no AGP present no redmine
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 41, context: html, text, full: html, text

2d7985fc8afa371efe6ea26acef924216383bd18 Wed Dec 29 12:43:15 2021 -0800

• best correspondence list for all hubs now complete no redmine
  • src/hg/makeDb/doc/zoonomiaAsmHub/zoonomia.orderList.tsv - lines changed 9, context: html, text, full: html, text

1aa2bfd8c15486f23f6efeec5f4358f366cfad53 Wed Dec 29 12:45:41 2021 -0800

• updated scripts to tolerate database assemblies in the listings no redmine
  • src/hg/makeDb/doc/asmHubs/mkAsmStats.pl - lines changed 60, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkSendList.pl - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/trackData.pl - lines changed 159, context: html, text, full: html, text

7709543f2b32e708d9c9f39334d452d6c52482f6 Wed Dec 29 12:46:40 2021 -0800

• temporarily turn off push to dynablat machine until more disk space is obtained no redmine
  • src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh - lines changed 12, context: html, text, full: html, text

d7d1c06cce94bfb5abced6d45f2f6ad3e2dbd2db Wed Dec 29 12:47:26 2021 -0800

• updated scripts to tolerate database assemblies in the listings no redmine
  • src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh - lines changed 22, context: html, text, full: html, text

110e0750597f5a80bd93e9bea4312428d9f92182 Wed Dec 29 13:00:08 2021 -0800

• updated to use assembly hubs that do not have database assemblies on the RR no redmine
  • src/hg/makeDb/doc/zoonomiaAsmHub/zoo241.asmId.sciName.tsv - lines changed 9, context: html, text, full: html, text

ce6a8cb8e1eeaa44acef44a163feb17db12bea17 Fri Dec 31 11:09:54 2021 -0800

• updating a couple new primate assemblies no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 2, context: html, text, full: html, text

7c4e6702ec1521e9ec6808dcd201cb8b80e44693 Fri Dec 31 21:32:21 2021 -0800

• adding five new fish no redmine
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 6, context: html, text, full: html, text

9f169d8c921625fb5f806420dbda13524b8c4f85 Fri Dec 31 21:34:31 2021 -0800

• adding new mammals and fish no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 16, context: html, text, full: html, text

42baee4d6187208718981a8cd42d699fe7e34a73 Fri Dec 31 22:07:56 2021 -0800

• a couple outdated mammal assemblies no redmine
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 2, context: html, text, full: html, text

538e939377d7a736914c2a1cdce300a0a0b8b06a Sat Jan 1 15:47:22 2022 -0800

• adding 11 new fungi no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 10, context: html, text, full: html, text

b9b0a57e12ac267d701445d9f738f23e2edfa30f Sat Jan 1 15:53:16 2022 -0800

• adding 11 new fungi no redmine
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 12, context: html, text, full: html, text

2f1373c09ad0c6ba9067e58717dd31aeee05c576 Tue Jan 4 21:03:39 2022 -0800

• adding 21 new invertebrates no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 21, context: html, text, full: html, text

9719e1a0ead12c9fa95a82d0f1e1a119f3fdbcc1 Tue Jan 4 21:04:33 2022 -0800

• adding 6 new plants no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 6, context: html, text, full: html, text

97e0b5f2881c91ae5dbc87f6eea3e19993545d09 Thu Jan 6 14:07:36 2022 -0800

• adding a second very large wheat genome no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text

6988d80500be7cd9ea274ef1a70b732c37e655c7 Thu Jan 6 14:08:26 2022 -0800

• adding a few new plant assemblies no redmine
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 8, context: html, text, full: html, text

a6478f571b96b1f4c65eb6c10e9750063d58d9df Thu Jan 6 14:09:20 2022 -0800

• adding new invertebrate assemblies no redmine
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 21, context: html, text, full: html, text

8a4f3a1b26c3cbba02413ad0c16f9d0a6d2d4c62 Thu Jan 6 14:10:01 2022 -0800

• a couple of plant assemblies aged out no redmine
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 2, context: html, text, full: html, text

3d845ef5b4ab847b7d2b6770f10af29023b09760 Thu Jan 6 14:11:12 2022 -0800

• catching up a few new mammal assemblies no redmine
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 12, context: html, text, full: html, text